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Detailed information for vg0323490253:

Variant ID: vg0323490253 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 23490253
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 350. )

Flanking Sequence (100 bp) in Reference Genome:

TTCTTTTGAACCTTAGACTGGGTTTGAAACTTAACATTATGATCTGCAGGTTGGAGACATGCAAAAGCGAGGCATATCGGAGGCCTTCAAGGTGAAGCAA[G/T]
CCATCCTTCTCTCCGCCACCGAGGCGGCTGAGATGATTCTCAGGGTTGATGAGATCATAACTTGTGCCCCACGCAGGAGAGAGGATAGGATGTGATCACA

Reverse complement sequence

TGTGATCACATCCTATCCTCTCTCCTGCGTGGGGCACAAGTTATGATCTCATCAACCCTGAGAATCATCTCAGCCGCCTCGGTGGCGGAGAGAAGGATGG[C/A]
TTGCTTCACCTTGAAGGCCTCCGATATGCCTCGCTTTTGCATGTCTCCAACCTGCAGATCATAATGTTAAGTTTCAAACCCAGTCTAAGGTTCAAAAGAA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	85.50%	12.40%	2.12%	0.00%	NA
All Indica	2759	99.60%	0.30%	0.04%	0.00%	NA
All Japonica	1512	61.70%	32.30%	6.02%	0.00%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	99.00%	0.90%	0.13%	0.00%	NA
Temperate Japonica	767	82.90%	10.00%	7.04%	0.00%	NA
Tropical Japonica	504	29.00%	67.10%	3.97%	0.00%	NA
Japonica Intermediate	241	62.70%	30.30%	7.05%	0.00%	NA
VI/Aromatic	96	25.00%	70.80%	4.17%	0.00%	NA
Intermediate	90	73.30%	22.20%	4.44%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0323490253	G -> T	LOC_Os03g42220.1	missense_variant ; p.Ala495Ser; MODERATE	nonsynonymous_codon ; A495S	Average:76.788; most accessible tissue: Callus, score: 86.974	benign	0.579	TOLERATED	0.33
vg0323490253	G -> T	LOC_Os03g42220.2	missense_variant ; p.Ala470Ser; MODERATE	nonsynonymous_codon ; A470S	Average:76.788; most accessible tissue: Callus, score: 86.974	benign	0.579	TOLERATED	0.31
vg0323490253	G -> T	LOC_Os03g42220.3	missense_variant ; p.Ala371Ser; MODERATE	nonsynonymous_codon ; A371S	Average:76.788; most accessible tissue: Callus, score: 86.974	benign	0.563	TOLERATED	0.34

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0323490253	NA	2.30E-13	Grain_thickness	Jap_All	YES	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0323490253	NA	6.45E-06	mr1029	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0323490253	NA	5.78E-06	mr1189	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0323490253	NA	8.70E-07	mr1642	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0323490253	4.02E-06	NA	mr1679	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0323490253	3.19E-06	3.18E-06	mr1815	Jap_All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0323490253	NA	5.95E-07	mr1554_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251